I agree with much of your take on medications, and I wonder whether there is some parallel with genes. That is, it's hard to find a gene whose expression only affects one thing, just as it is hard to find a medication that only affects one functional body system or impacts one disorder. And hard to find a cluster of neurons that only affects one functional outcome. Aren't all of these to some extent consequences of one of the more standard but less intuitive ramifications of evolution: that new features rarely arise, except by building on and exploiting existing ones? So when we define a physiological outcome, unless we happen to get it right regarding its historical origin, we are always subject to serious surprises about how things are connected together. Perhaps that's why when you deal with something particuarly ancient, like serotonergic transmission; looking for something like anti-depressant effects or again something like appetite suppression; you end up with global effects on remote things like the gut and the heart valves (Phen-Fen). We take "side effects" pretty much for granted as a reality of medication, but they wouldn't happen so seemingly randomly if medications were as targeted in their effect as we tend to assume, I would think. A big claim of pharm companies is that their psychoactive drugs are becoming more and more targeted because they affect more and more specific neurotransmitter and neuromodulator systems, but they still come up with very unexpected side effects.
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